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Detailed information for vg0211479975:

Variant ID: vg0211479975 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 11479975
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTGACTTGGGGACAAAACATGAATCAATTATTACATGTTTTCTCAGCTTGGGGTAATTCAAAATGTTTGACACCGTTGACTTTTTAGTATATGTTTGAC[C/T]
GTTCGTCTTATTAAAAAAATTTATGAAATATGTAAAACTATATGTATACATGAAATTATATTTAACAATGAATCAAATGATATGAAAAGAATTAATAATT

Reverse complement sequence

AATTATTAATTCTTTTCATATCATTTGATTCATTGTTAAATATAATTTCATGTATACATATAGTTTTACATATTTCATAAATTTTTTTAATAAGACGAAC[G/A]
GTCAAACATATACTAAAAAGTCAACGGTGTCAAACATTTTGAATTACCCCAAGCTGAGAAAACATGTAATAATTGATTCATGTTTTGTCCCCAAGTCACC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.50%	2.40%	0.06%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	92.30%	7.50%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	89.60%	10.00%	0.39%	0.00%	NA
Tropical Japonica	504	97.40%	2.60%	0.00%	0.00%	NA
Japonica Intermediate	241	90.00%	10.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0211479975	C -> T	LOC_Os02g19650.1	downstream_gene_variant ; 4355.0bp to feature; MODIFIER	silent_mutation	Average:72.949; most accessible tissue: Callus, score: 92.869	N	N	N	N
vg0211479975	C -> T	LOC_Os02g19650.3	downstream_gene_variant ; 4353.0bp to feature; MODIFIER	silent_mutation	Average:72.949; most accessible tissue: Callus, score: 92.869	N	N	N	N
vg0211479975	C -> T	LOC_Os02g19640.1	intron_variant ; MODIFIER	silent_mutation	Average:72.949; most accessible tissue: Callus, score: 92.869	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0211479975	4.67E-06	4.67E-06	mr1935	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0211479975	NA	1.38E-06	mr1305_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0211479975	NA	1.30E-06	mr1585_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251